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- PDB-1gng: Glycogen synthase kinase-3 beta (GSK3) complex with FRATtide peptide -

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Basic information

Entry
Database: PDB / ID: 1gng
TitleGlycogen synthase kinase-3 beta (GSK3) complex with FRATtide peptide
Components
  • FRATTIDE
  • GLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE / PROTEIN KINASE / GSK3-FRATTIDE COMPLEX / PHOSPHORYLATED / ACTIVE
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / regulation of axon extension / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / tau-protein kinase activity / positive regulation of cell-matrix adhesion / regulation of axonogenesis / molecular function inhibitor activity / regulation of dendrite morphogenesis / ER overload response / glycogen metabolic process / regulation of neuron projection development / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / negative regulation of canonical Wnt signaling pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / beta-catenin binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / circadian rhythm / cellular response to amyloid-beta / positive regulation of protein catabolic process / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of protein binding / kinase activity / p53 binding / positive regulation of canonical Wnt signaling pathway / positive regulation of neuron apoptotic process / insulin receptor signaling pathway
Similarity search - Function
Glycogen synthase kinase-3 binding protein / Glycogen synthase kinase-3 binding / Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Glycogen synthase kinase-3 binding protein / Glycogen synthase kinase-3 binding / Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycogen synthase kinase-3 beta / Proto-oncogene FRAT1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBax, B. / Carter, P.S. / Lewis, C. / Guy, A.R. / Bridges, A. / Tanner, R. / Pettman, G. / Mannix, C. / Culbert, A.A. / Brown, M.J.B. ...Bax, B. / Carter, P.S. / Lewis, C. / Guy, A.R. / Bridges, A. / Tanner, R. / Pettman, G. / Mannix, C. / Culbert, A.A. / Brown, M.J.B. / Smith, D.G. / Reith, A.D.
CitationJournal: Structure / Year: 2001
Title: The Structure of Phosphorylated Gsk-3Beta Complexed with a Peptide, Frattide, that Inhibits Beta-Catenin Phosphorylation
Authors: Bax, B. / Carter, P.S. / Lewis, C. / Guy, A.R. / Bridges, A. / Tanner, R. / Pettman, G. / Mannix, C. / Culbert, A.A. / Brown, M.J.B. / Smith, D.G. / Reith, A.D.
History
DepositionOct 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 285 THE SPACE-GROUP H 3 2 IS THE HEXAGONAL SETTING OF R 3 2 (NO 155)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: GLYCOGEN SYNTHASE KINASE-3 BETA
X: FRATTIDE
Y: FRATTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8459
Polymers95,3394
Non-polymers5065
Water2,522140
1
A: GLYCOGEN SYNTHASE KINASE-3 BETA
X: FRATTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8624
Polymers47,6692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLYCOGEN SYNTHASE KINASE-3 BETA
Y: FRATTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9845
Polymers47,6692
Non-polymers3143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)153.050, 153.050, 213.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / GSK3B


Mass: 43126.277 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49841, EC: 2.7.1.37
#2: Protein/peptide FRATTIDE


Mass: 4543.136 Da / Num. of mol.: 2 / Fragment: RESIDUES 188-226 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q92837
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNOTE RESIDUE 350 IS LEU (CF HIS IN SWISSPROT) SEE REFERENCE BIOCHEM. J. 303:701-704(1994)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: 1.6M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
2100 mMTris-acetate1reservoirpH8.2
3125 mM1reservoirNaCl
46-14 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorDate: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 29716 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 52.7 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 11 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 99.9 % / Num. measured all: 333047

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Processing

Software
NameClassification
CNSrefinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ERK

2erk


Resolution: 2.6→18 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 -5 %SHELLS
Rwork0.196 ---
obs0.196 29649 99.9 %-
Displacement parametersBiso mean: 53.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.93 Å24.15 Å20 Å2
2---4.93 Å20 Å2
3---9.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6059 0 28 140 6227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 224 4.6 %
Rwork0.291 4697 -
obs--100 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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